warp-md 0.1.3__tar.gz → 0.1.4__tar.gz

{warp_md-0.1.3 → warp_md-0.1.4}/Cargo.lock

@@ -587,11 +587,11 @@ dependencies = [
 
 [[package]]
 name = "traj-core"
-version = "0.1.3"
+version = "0.1.4"
 
 [[package]]
 name = "traj-engine"
-version = "0.1.3"
+version = "0.1.4"
 dependencies = [
  "bytemuck",
  "libloading",
@@ -606,7 +606,7 @@ dependencies = [
 
 [[package]]
 name = "traj-gpu"
-version = "0.1.3"
+version = "0.1.4"
 dependencies = [
  "cudarc",
  "traj-core",
@@ -615,7 +615,7 @@ dependencies = [
 
 [[package]]
 name = "traj-io"
-version = "0.1.3"
+version = "0.1.4"
 dependencies = [
  "tempfile",
  "traj-core",
@@ -624,11 +624,11 @@ dependencies = [
 
 [[package]]
 name = "traj-kernels"
-version = "0.1.3"
+version = "0.1.4"
 
 [[package]]
 name = "traj-py"
-version = "0.1.3"
+version = "0.1.4"
 dependencies = [
  "numpy",
  "pyo3",

warp_md-0.1.4/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Ayodele Ifeoluwa Faleti
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

warp_md-0.1.4/MANIFEST.in

@@ -0,0 +1,9 @@
+include Cargo.toml
+include Cargo.lock
+include pyproject.toml
+include README.md
+include LICENSE
+recursive-include crates *
+recursive-include python *
+recursive-include scripts *
+recursive-include docs *

{warp_md-0.1.3 → warp_md-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: warp-md
-Version: 0.1.3
+Version: 0.1.4
 Requires-Dist: numpy
 Requires-Dist: pyyaml ; extra == 'cli'
 Provides-Extra: cli

warp_md-0.1.4/README.md

@@ -0,0 +1,89 @@
+# warp-md
+
+CPU-first MVP scaffold for MD trajectory IO + analysis, with optional CUDA path.
+
+## Status
+
+- Rust workspace scaffolded with core, IO, engine, GPU stub, kernels placeholder, and PyO3 bindings.
+- Implemented: PDB/GRO topology readers, DCD reader (32/64-bit markers, best-effort unit cell), XTC reader (xdrfile), selection engine, CPU Rg/RMSD/MSD/RDF, polymer analyses (end-to-end, contour length, chain Rg, bond length/angle distributions, persistence length), and analysis suite (rotational ACF, conductivity, dielectric, dipole alignment, ion-pair correlation, structure factor, water grid, equipartition temperature, H-bond counts).
+- Correlator plans use streaming multi-tau by default (bounded memory); ring-buffer and FFT modes are available for short-time exactness or small streams.
+- Feature store support: chunked binary + JSON index for offline/long-run feature capture (`feature_store` module).
+- CUDA: optional GPU path (per-frame feature extraction and kernels) behind `--features cuda` and requires CUDA driver + nvrtc at runtime. Persistence length and parts of the analysis suite remain CPU reductions for now.
+
+## Build and test
+
+Rust:
+
+```bash
+cargo test
+```
+
+CUDA build (requires CUDA runtime libraries present):
+
+```bash
+cargo test -p traj-engine --features cuda
+```
+
+If the CUDA toolkit isn't detected, set `CUDA_HOME` (or `CUDA_PATH`) so `cudarc` can resolve the version.
+
+Python (requires maturin):
+
+```bash
+maturin develop
+python -c "import warp_md; print(warp_md.System)"
+```
+
+## Python usage (CPU)
+
+```python
+from warp_md import System, Trajectory, RgPlan, EndToEndPlan, MsdPlan
+
+system = System.from_pdb("example.pdb")
+selection = system.select("name CA")
+traj = Trajectory.open_dcd("traj.dcd", system)
+plan = RgPlan(selection, mass_weighted=False)
+rg = plan.run(traj, system, device="auto")
+poly = EndToEndPlan(selection)
+end_to_end = poly.run(traj, system, device="auto")
+msd = MsdPlan(selection, group_by="resid")
+time, data = msd.run(traj, system)
+```
+
+## CLI (Python)
+
+Single-command CLI for agents, plus config-driven runs.
+
+```bash
+# one-command analysis
+warp-md rg --topology top.pdb --traj traj.xtc --selection "protein"
+warp-md rdf --topology top.pdb --traj traj.xtc --sel-a "resname SOL and name OW" --sel-b "resname SOL and name OW" --bins 200 --r-max 10
+
+# config runner
+warp-md example > config.json
+warp-md run config.json
+warp-md list-plans
+```
+
+By default, the CLI prints a JSON summary to stdout. Use `--no-summary` to disable.
+YAML configs require `pip install warp-md[cli]`.
+
+## Documentation
+
+- Getting started and full walkthrough: `docs/tutorial.md`
+- Full API + module reference: `docs/reference.md`
+- Validation + accuracy comparison: `docs/validation.md`
+- Docs index: `docs/README.md`
+
+## Python builder helpers
+
+```python
+from warp_md import charges_from_table, group_types_from_selections
+
+charges = charges_from_table(system, "charges.tsv")
+group_types = group_types_from_selections(
+    system,
+    system.select("resname BMIM or resname BF4"),
+    "resid",
+    ["resname BMIM", "resname BF4"],
+)
+```

{warp_md-0.1.3 → warp_md-0.1.4}/crates/traj-core/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "traj-core"
-version = "0.1.3"
+version = "0.1.4"
 edition = "2021"
 license = "MIT"
 

{warp_md-0.1.3 → warp_md-0.1.4}/crates/traj-engine/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "traj-engine"
-version = "0.1.3"
+version = "0.1.4"
 edition = "2021"
 license = "MIT"
 
@@ -8,7 +8,7 @@ license = "MIT"
 traj-core = { path = "../traj-core" }
 traj-io = { path = "../traj-io" }
 nalgebra = "0.32"
-traj-gpu = { path = "../traj-gpu", optional = true }
+traj-gpu = { path = "../traj-gpu" }
 rustfft = "6.2"
 bytemuck = { version = "1.15", features = ["extern_crate_alloc"] }
 serde = { version = "1.0", features = ["derive"] }

warp_md-0.1.4/crates/traj-gpu/Cargo.toml

@@ -0,0 +1,13 @@
+[package]
+name = "traj-gpu"
+version = "0.1.4"
+edition = "2021"
+license = "MIT"
+
+[dependencies]
+traj-core = { path = "../traj-core" }
+traj-kernels = { path = "../traj-kernels" }
+cudarc = { version = "0.19", optional = true, features = ["driver", "nvrtc", "cuda-12040"] }
+
+[features]
+cuda = ["cudarc"]